# Flexible Genotyping for Polyploids

## Documentation for package ‘updog’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

updog-package | 'updog' Flexible Genotyping for Polyploids
betabinom | The Beta-Binomial Distribution
convolve_up | Convolution between two discrete probability mass functions with support on 0:K.
dbetabinom | The Beta-Binomial Distribution
flexdog | Flexible genotyping for polyploids from next-generation sequencing data.
flexdog_full | Flexible genotyping for polyploids from next-generation sequencing data.
format_multidog | Return matricized elements from the output of 'multidog'.
get_bivalent_probs | Returns segregation probabilities, pairing representation and number of ref alleles given the ploidy.
get_hyper_weights | Return mixture weights needed to obtain a hypergeometric distribution.
get_q_array | Return the probabilities of an offspring's genotype given its parental genotypes for all possible combinations of parental and offspring genotypes. This is for species with polysomal inheritance and bivalent, non-preferential pairing.
is.flexdog | Tests if an argument is a 'flexdog' object.
is.multidog | Tests if an argument is a 'multidog' object.
is.mupdog | Tests if its argument is a mupdog object.
log_sum_exp | Log-sum-exponential trick.
log_sum_exp_2 | Log-sum-exponential trick using just two doubles.
multidog | Fit 'flexdog' to multiple SNP's.
mupdog | Using correlation between individuals for genotyping.
mupout | A mupdog fit of the 'uitdewilligen' data.
oracle_cor | Calculates the correlation between the true genotype and an oracle estimator.
oracle_cor_from_joint | Calculate the correlation of the oracle estimator with the true genotype from the joint distribution matrix.
oracle_joint | The joint probability of the genotype and the genotype estimate of an oracle estimator.
oracle_mis | Calculate oracle misclassification error rate.
oracle_mis_from_joint | Get the oracle misclassification error rate directly from the joint distribution of the genotype and the oracle estimator.
oracle_mis_vec | Returns the oracle misclassification rates for each genotype.
oracle_mis_vec_from_joint | Get the oracle misclassification error rates (conditional on true genotype) directly from the joint distribution of the genotype and the oracle estimator.
oracle_plot | Construct an oracle plot from the output of 'oracle_joint'.
pbetabinom | The Beta-Binomial Distribution
plot.flexdog | Draw a genotype plot from the output of 'flexdog'.
plot.multidog | Plot the output of 'multidog'.
plot.mupdog | Draw a genotype plot from the output of 'mupdog'.
plot_geno | Make a genotype plot.
qbetabinom | The Beta-Binomial Distribution
rbetabinom | The Beta-Binomial Distribution
rflexdog | Simulate GBS data from the 'flexdog' likelihood.
rgeno | Simulate individual genotypes from one of the supported 'flexdog' models.
snpdat | GBS data from Shirasawa et al (2017)
summary.mupdog | Provides some summaries from the output of 'mupdog'.
uitdewilligen | Subset of individuals and SNPs from Uitdewilligen et al (2013).
updog | 'updog' Flexible Genotyping for Polyploids
wem | Generalized version of 'uni_em'.